Ubuntu Manpage: anfo - find best alignment of short reads to database

NAME

       anfo - find best alignment of short reads to database

SYNOPSIS

       anfo [ option | file ... ]

DESCRIPTION

       anfo aligns (short) sequencing reads to a (gigabase sized) database.  It uses a heuristic seeding method,
       but then applies a genuine aligner that allows gaps, understands  damage  patterns  in  ancient  dna  and
       produces an easy to interpret score.

       Input  files  can  be  any  variety  of  FastA  or  FastQ  files, or a native anfo binary file, optinally
       compressed using gziporbzip2.  The file format is automatically  recognized  and  other  formats  may  be
       added.

OPTIONS

-V, --version
Print version number and exit.

-o file, --output file
Write output to file. file will be written in the native anfo binary format, which can be operated
upon using anfo-tool or the bindings to guile.

-c conffile, --config conffile
Read configuration from conffile. This file configures which indices are used, and by extension
to which genomes an alignment is made, what parameters to use in the aligner and can set paths.
See the example file.

-p num, --threads num
Start num threads for alignment. One such thread per processor core is usually best.

-x num, --ixthreads num
Start num threads for indexing. Indexing normally uses less cpu power than alignment, so fewer
indexers than aligners is normally best.

--solexa-scale
When reading FastQ files, use the Solexa scale (log-odds-ratios) instead of the standard Phread
scale (probabilities). If you use Solexa/Illumina sequencers, refer to your documentation whether
you need this. Else you don't.

--fastq-origin ori
Set origin for FastQ decoding to ori. The standard and default is 33, but it must be set to 64
for some versions of the Solexa/Illumina software. If you use Solexa/Illumina sequencers, refer
to your documentation whether you need this. Else you don't.

-q, --quiet
Suppress all output except fatal errors.

-v, --verbose
Print a progress indicator during operation.

ENVIRONMENT

       ANFO_PATH
              Colon separated list of directories searched for genome and index files.

FILES

       /etc/popt
              The system wide configuration file for popt(3).  anfo identifies itself as "anfo" to popt.

       ~/.popt
              Per user configuration file for popt(3).

       /usr/share/doc/anfo/example/*.cfg
              Example configuration files to be used with anfo.

BUGS

       None known.

AUTHOR

       Udo Stenzel <udo_stenzel@eva.mpg.de>